Start Page
Pfam Identifier
Enter the identifier for the Pfam-A family you are interested in, with or without the leading 'PF' chars. Currently, this service does not include Pfam-B.
By default, after clicking 'search', you will be shown a list of families containing alignments to your query family, with descriptions, mean scores and links to Pfam - you may then select which families you wish to view alignments for. To skip this stage and automatically grab alignments for all hits, select the radio-button 'fetch alignment using all hits'.
Maximum hits
This parameter controls how many hits are displayed in the results page. You should be aware that the higher this number, the more time it will take to return your results.
Expand Gaps
The alignment returned is not a true multiple alignment, but rather, a pile-up alignment with each hit aligned to the representative of your query family (at the very top of the alignment). By default, any insertions in hit proteins which would open a gap in the query sequence will not be displayed - this is a quick way to see the key motifs in your alignment, but please be aware that hit sequences may not be contiguous, even though they appear to be. If you select the 'yes' radio-button, all insertions in hit sequences will be expanded throughout the alignment, and the sequences will be contiguous. However, this can make the alignment considerably wider, and it will be less easy to spot the key motifs.
Score Thresholds
Pfam-Squared uses two scoring systems - motif, a weighted residue-identity score, and gtg, a score based on neighbourhood overlap along the alignment trace. The combined score is a combination of the two in the ratio 80:20, motif:gtg. To exclude spurious hits with low scores, you can set score thresholds for any of the three scores.
Family Selection Page
The parameters that were chosen on the start page are displayed at the top of the selection page. If you've changed your mind you can alter them here, otherwise, leave them as they are.
Making Your Selection
Select or deselect families to align using the check-boxes (note that the 'deselect all' button only works with javascript enabled). The alignment scores displayed are mean scores, averaged over all alignments between query and hit families - they give an initial indication of how closely related the families are. If score thresholds are set, only those hits that exceed the threshold will be shown in the alignment page. Once you have made your selection, click 'view alignment', and wait. Note that this can take quite a few seconds if the 'Expand Gaps' parameter is set, and/or if the 'Max Hits' parameter is large - please be patient.
Result Page
Fields and Links
There are a few header fields before the alignment section - these are:
  • identifier - usually UNIPROT or PIR id/accession - linked to the original database entry
  • nid - numerical identifier for the sequence from our non-redundant database, PairsDB - linked to ADDA Domain page
  • family - identifier of Pfam-A family to which this protein belongs - linked to Pfam website entry
  • clan - identifier of Pfam clan to which this protein belongs (if any) - linked to Pfam website entry
  • motif - motif score for the alignment between this sequence and the query
  • gtg - gtg score for the alignment between this sequence and the query
  • combi - combined score for the alignment between this sequence and the query
The alignment section itself starts and ends with the from/to values for each hit sequence. The alignment is coloured using the default ClustalX Colour Scheme.
Finally, the description from the original sequence database entry is given for each hit, after the alignment section.
Resize Your Alignment
You can alter the text size of your alignment if it renders too large or small at your screen resolution - just click the appropriate link at the top of the page.
Other Notes
Please note that different browsers cope with long, unwrapped strings of characters in wildly different ways. Therefore, very long alignments will be split into (at least two) sections, to ensure they display correctly. Scroll down the page to see the other sections. If your alignment appears oddly rendered or messed up in any way, please send us an email telling us what browser and operating system you are using, and we will try to correct the problem.